I found the old top to the RPi case (the same one you purchased) with the fan still mounted - I've attached a photo. You'll see two of the standard fan mounting pegs above where the fan is mounted - obviously not being used in order to provide clearance for the RTC. If I recall correctly, I may have had to clip/grind the other two pegs down so I could move the fan. The four screws go into the vent slots and firmly hold the fan inside the case. The cover fits just fine with the fan inside the case, not mounted outside and not interfering with the case closing all the way.